I have a big protein with low conservation with PDB files. So I increased simulation with -light true -hours 400 but I-TASSER shows 15! The following is I-TASSER 4.1 run Information. I have altered the sequence and template to ***.
Your setting for running I-TASSER is:
-pkgdir = /home/arman/I-TASSER4.1
-libdir = /home/arman/ITLIB
-java_home = /usr
-seqname = seq
-datadir = /home/arman/Dropbox/4408-Shahrisa/IT400
-outdir = /home/arman/Dropbox/4408-Shahrisa/IT400
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 50
-nmodel = 10
-light = true
-hours = 400
-LBS = true
-EC = true
-GO = false
1. make seq.txt and rmsinp
Your protein contains 458 residues:
> seq
***
2.1 run Psi-blast
2.2 Predict secondary structure with PSSpred...
2.3 Predict solvent accessibility...
2.4 run pairmod
2.4.1 Use all templates
2.4.2 running pair ................
FORTRAN STOP
30000 6379375 total lib str & residues
number of observations 14.15487 8907549.
pair done
3.1 do threading
start serial threading PPAS
/tmp/arman/ITseq
/home/arman/Dropbox/4408-Shahrisa/IT400/PPAS_seq
hostname: U
starting time: Sun Sep 14 16:38:46 IRDT 2014
pwd: /tmp/arman/ITseq
running zalign .....
ending time: Sun Sep 14 17:13:05 IRDT 2014
start serial threading dPPAS
/tmp/arman/ITseq
/home/arman/Dropbox/4408-Shahrisa/IT400/dPPAS_seq
hostname: U
starting time: Sun Sep 14 17:13:08 IRDT 2014
pwd: /tmp/arman/ITseq
running zalign .....
ending time: Sun Sep 14 19:32:12 IRDT 2014
start serial threading dPPAS2
/tmp/arman/ITseq
/home/arman/Dropbox/4408-Shahrisa/IT400/dPPAS2_seq
hostname: U
starting time: Sun Sep 14 19:32:16 IRDT 2014
pwd: /tmp/arman/ITseq
running zalign .....
ending time: Sun Sep 14 21:55:15 IRDT 2014
start serial threading Env-PPAS
/tmp/arman/ITseq
/home/arman/Dropbox/4408-Shahrisa/IT400/Env-PPAS_seq
hostname: U
starting time: Sun Sep 14 21:55:26 IRDT 2014
pwd: /tmp/arman/ITseq
running zalign .....
ending time: Mon Sep 15 18:49:25 IRDT 2014
start serial threading MUSTER
/tmp/arman/ITseq
/home/arman/Dropbox/4408-Shahrisa/IT400/MUSTER_seq
hostname: U
starting time: Mon Sep 15 18:49:40 IRDT 2014
pwd: /tmp/arman/ITseq
running Psi-blast .....
running zalign .....
==>*** *** 10.4962321332816 9.80217696981886
*** *** 19 16
score_flag=1
ending time: Mon Sep 15 20:51:07 IRDT 2014
start serial threading wPPAS
/tmp/arman/ITseq
/home/arman/Dropbox/4408-Shahrisa/IT400/wPPAS_seq
hostname: U
starting time: Mon Sep 15 20:51:13 IRDT 2014
pwd: /tmp/arman/ITseq
running Psi-blast .....
ending time: Mon Sep 15 22:12:37 IRDT 2014
start serial threading wdPPAS
/tmp/arman/ITseq
/home/arman/Dropbox/4408-Shahrisa/IT400/wdPPAS_seq
hostname: U
starting time: Mon Sep 15 22:12:42 IRDT 2014
pwd: /tmp/arman/ITseq
running Psi-blast .....
ending time: Tue Sep 16 15:59:19 IRDT 2014
start serial threading wMUSTER
/tmp/arman/ITseq
/home/arman/Dropbox/4408-Shahrisa/IT400/wMUSTER_seq
hostname: U
starting time: Tue Sep 16 15:59:22 IRDT 2014
pwd: /tmp/arman/ITseq
running Psi-blast .....
running Psi-blast .....
==>*** *** 13.8016723201232 12.8799825039397
*** *** 19.87 19.87
score_flag=1
ending time: Tue Sep 16 18:24:14 IRDT 2014
3.2 make restraints
type= easy, n_good=40, M0= 8, M1_for_medm=1.6, n_sg= 8 role=SEQ
1 gap_terminal=N gap_location= 98 by MUSTER
2 gap_terminal=N gap_location= 98 by dPPAS
3 gap_terminal=N gap_location= 98 by wdPPAS
4 gap_terminal=N gap_location= 99 by wMUSTER
5 gap_terminal=N gap_location= 98 by wPPAS
6 gap_terminal=N gap_location= 98 by dPPAS2
7 gap_terminal=N gap_location= 98 by PPAS
8 gap_terminal=N gap_location= 98 by Env-PPAS
9 gap_terminal=N gap_location=100 by dPPAS
10 gap_terminal=N gap_location=100 by dPPAS2
11 gap_terminal=N gap_location=100 by PPAS
12 gap_terminal=N gap_location=100 by Env-PPAS
domain2=yes
------ n_link_old= 98-------------
------ 2 domain proteins: 98-------------
type=easy----n_temp_use_for_restraints=20
4.1 run simulation
run 15 serial simulations
run simulation job 1 / 15
The simulation continues in my pc.